In the season opener played at the National Stadium, Abuja, ended goalless after 90 minutes before Akwa United won 4-3 via penalty shootout.
Akwa United was impressive in defence, holding Enyimba to a draw despite playing with 10-men after Yusuf Adio was sent off in the 65th minute.
Coach Maurice Cooreman led side will now enter the NPFL season as one of the most in-form teams in the country.
They drew with Enyimba some few weeks ago to win the Super Four tournament organised by the League Management Company.
Akwa United also beat the likes of Warri Wolves and Nasarawa to win the Super Four.
They also beat Vita Club Mokanda of Congo 1-0 in Pointe Noir in a CAF Confederation Cup first round, first leg match.
Akwa United will travel to face Sunshine Stars in the opening week of the NPFL 2016 season while Enyimba game is an away trip to Dolphins of Port Harcourt.